Skip to main content

Column exchange script in Python

This script allows one to exchange two columns in a file.And it do so for all the files in a directory. The python script is :

----------------------------

#script to read and execute column exchange for all files in the directory
import os
listing=os.listdir("/home/K/Documents/PY/column_exchange")
for infile in listing:
 print infile
 if infile !="column_interchange_script.py":
  fi=open(infile).readlines()
  fo=open(infile +'_output','w')
  space="   "
  for line in fi:
   first,second=line.split()
   fo.write('%s%s%s\n'%(second,space,first))
 else:
   print "This is not interesting file"
   
----------------------------------------------------
 
 Some expert might simplify it a lot more, but for new python user like me, this is a big leap.
So, how does it work:

Create a directory where in all the files for which column exchange need to be done are stored.
Keep this python script also in the same directory.
The path shown in bold  need to be replaced with the proper path of the directory.
$python column_interchange_script.py command shoulf carry out column exchange for all the files in the directory.



One problem I was facing was the script was reading itself also and collapsing with an error. So I added exception using "!=" returning result for it with else statement.


One precaution: if you modify the script using editor, then it creates a temprary file column_interchange_script.py~ sometimes. This could create problem. script reads this file also and collapses. So either modify it in terminal or delete this file.

Why I needed this?
The Umbrella Sampling calculations yield files with values in two columns. For plotting individual histograms corresponding to each file we need to exchange columns. Number of such files might be large enough to motivate you to write a script to do so.
I have few things in mind to improvise on it, but since my task is fulfilled with this script, I might not modify it any further
 

Comments

Popular posts from this blog

Material Studio - selective molecule movement

So, working with Material Studio is awesome. You get to handle bigger, complicated and even unimaginable system. But I am facing problems in very minute functioning. I recently faced two problems, but managed to resolve on my own. Somehow, tutorials doesn't help in resolving them and you end up doing some exercise on your own to get the solution. Among these, the problem of bringing two molecular structures in one window and then adjusting one molecule by moving it around, while other structure remains untouched, as it is. Actually, this should not be a problem to do. There is a simple way of doing this. Select the molecule to be moved and then there is a symbol (button) to select, which allows you to selectively move that molecule only. This is the same way it can be done in Material studio too.  But among all the dozens of symbols, the new person handling MS, kind of gets lost. So, what he does is check the tutorials, for any help. But the tutorials don't talk about suc...

Using Packmol

Packmol is a software that allows you to generate a single combined PDB file for all the molecules you are considering. It is a free software and can be downloaded from this link: http://www.ime.unicamp.br/~martinez/packmol/ The installation guide is also provided on the page and its really easy to follow. http://www.ime.unicamp.br/~martinez/packmol/ You can also find some examples but I tried on my own. Anyway what you need is an input file which looks like: ------------------ tolerance 2.0 output trial.pdb add_amber_ter filetype pdb structure 2a.pdb   number 1   inside cube 0. 0. 0. 10. end structure structure 2d.pdb   number 1   inside cube 0. 0. 0. 10. end structure --------------------------------- IT includes some information like: how close the molecules considered can be.(tolerance) name of output pdb file "add_amber_ter" adds term "TER" after every molecule thus defining the start and end of every molecule. After mentioning the...

AutoDock Vina protocol: For Molecular Docking

There are many softwares available for carrying out molecular docking calculations. Many of these softwares are paid, while some of them are free. AutoDock is one such freely available software. Earlier, there was AutoDock 4.0 version available. One of the problem with the software was the space it would occupy, if you attempt to do multi docking. Recently, there is another algorithm made available under autodock. It is called AutoDock Vina. This is more efficient, robust and fast algorithm. There are many tutorials available to learn AutoDock Vina including: http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools/2012_ADTtut.pdf and also a video tutorial http://vina.scripps.edu/tutorial.html    But for some reason, few changes or explanation in little detail is always required to make it understandable for a beginner to follow.  Here is a protocol designed in our group, which our Master's student follow to get acquainted to Molecular...